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<b>Tian D</b>acheng

Professor

Tian Dacheng Ph.D

Office: Life Science Building B419

Phone:+86-025-89686406

Fax:+86-025-83592705

E-mail: dtian(at)nju.edu.cn

       

 

 

 

 

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Research Interests
    A fundamental problem in evolutionary biology is how genetic variation is created and maintained. My research focuses on this problem, although we are also interested in other issues of evolutionary genomics. The comparative genomics has revealed that there are lots of insertions/deletions (indels) between genomes. Our approach differs from the traditional evolutionary genomics, where the indels (asymmetric DNA segments) are largely neglected. Our integrated approach allows us to derive more testable predictions so that we can study both details and broad perspectives in the evolution of these sequence segments. Our goal is to understand the role that the asymmetric DNA plays in and its evolutionary dynamics. Another research focus is to understand the variation pattern and the characteristics of rice R-genes. R-genes are extremely polymorphic; therefore, the evolutionary mechanism maintaining such high level of polymorphism has long been controversial. By comparing sequences between two rice genomes and sequencing R-genes among wild rice and cultivars, we have obtained evidence that such extreme polymorphism is maintained by genetic isolation at the molecular level.

Education
    Ph.D. (1997) Department of Biological Sciences, University of Newcastle, Australia
    Ph.D. (1993) Department of Agronomy, Nanjing Agricultural University, China
    M.S. (1986) Department of Agronomy, Sichuan Agricultural University, China

Professional Experience
    1998-2003 Research Associate, Department of Ecology and Evolution, University of Chicago
    1997-1998 Research Scientist, ForBio Research, Australia
    1993-1994 Associate professor in Rice Research Institute, Sichuan Agricultural University
    1986-1993 Research Director, Senior Agronomist in Sichuan Provincial Seed Company

Selected publications
    Yang S, Wang L, Huang J, Zhang X, Yuan Y, Chen J-Q, Hurst LD*, Tian D* (2015). Parent-progeny sequencing indicates higher mutation rates in heterozygotes. Nature 523: 463–467
    Tian D*, Wang Q, Zhang P, Araki H, Yang S, Kreitman M, Nagylaki T, Hudson R, Bergelson J & Chen JQ. (2008) Single-nucleotide mutation rate increases close to indels in eukaryotes. Nature 455:105-108
    Tian D, Shaw B, Chen J, Kreitman M, Bergelson J (2003) Fitness cost of R-gene mediated resistance in Arabidopsis thaliana. Nature 424:74-77
    Bergelson J, Kreitman M, Stahl E, Tian D (2001) Evolutionary dynamics of plant R-genes. Science 292:2281-2285
    Yang S, Li J, Zhang XH, Zhang QJ, Huang J, Chen JQ, Hartl DL, Tian D*. (2013) Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease. Proc Natl Acad Sci 110: 18572-18577
    Yang S, Yuan Y, Wang L, Li J, Wang W, Liu H, Chen JQ, Hurst LD, Tian D*. (2012) Great majority of recombination events in Arabidopsis are gene conversion events. Proc Natl Acad Sci 109 :20992-20997
    Araki H, Tian D, Goss EM, Jakob K, Halldorsdottir SS, Kreitman M and Bergelson J. (2006) Presence/absence polymorphism for alternative pathogenicity islands in Pseudomonas viridiflava, a pathogen of Arabidopsis. Proc Natl Acad Sci 103:5587-5892
    Tian D, Akashi H, Stahl E, Bergelson J, Kreitman M (2002) Signature of balancing selection in Arabidopsis. Proc Natl Acad Sci 99:11525-1153
    Zhang X#, Yang S#, Wang J#, Jia Y#, Huang J#, Zhong Y, Tan S, Wang L, Gu L, Chen JQ, Pan QH*, Bergelson J*, Tian D* (2015). A genome-wide survey reveals abundant rice blast R-genes in resistant cultivars. Plant J 84 :20-28 (IF5y =6.963)
    Yue J-X, Meyers BC, Chen J-Q, Tian D*, Yang S. (2012) Tracing the origin and evolutionary history of plant nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes. New Phytologist 193: 1049–1063 (IF=6.736)
    Zhu L, Wang Q, Tang P, Araki H, Tian D*. (2009) Genome-wide association between insertions/deletions and the nucleotide diversity in bacteria. Mol Biol Evol 26:2353-2361 (IF=10.353)
    Chen JQ, Wu Y, Yang H, Bergelson J, Kreitman M, Tian D*. (2009) Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria. Mol Biol Evol 26:1523-31 (IF=10.353)
    Sun X, Zhang Y, Yang S, Chen JQ, Hohn B, Tian D* (2008) Insertion DNA promotes ectopic recombination during meiosis in Arabidopsis. Mol Biol Evol 25:2079-2083 (IF=10.353)
    Gu T, Tan S, Gou X, Araki H, Tian D*. (2010) Avoidance of long mononucleotide repeats in codon pair usage. Genetics 186:1077-1084
    Shen J, Araki H, Chen L, Chen JQ, Tian D* (2006) Unique evolutionary mechanism in R-genes under the presence/absence polymorphism in Arabidopsis thaliana. Genetics 172 (2):1243-50

Other publications
    Li J, Zhou J, Wu, Y, Yang S, Tian D*. (2015) GC-content of synonymous codons profoundly infulences amino acid usage. G3 : Genes|Genomes|Genetics 5(10):2027-36
    Tan S, Zhong Y, Hou H, Yang S, Tian D. (2012) Variation of presence/absence genes among Arabidopsis populations. BMC Evol Biol 12:86
    Wang L, Si W, Yao Y, Tian D, Araki H. Yang S. (2012) Genome-wide survey of pseudogenes in 80 fully re-sequenced Arabidopsis thaliana accessions. Plos One 7(12): e51769
    Tan S, Wang D, Ding J, Tian D, Zhang XH, Yang S. (2011) Adaptive evolution of Xa21 homologs in gramineae. Genteica 139:1465-1475
    Wang J, Zhang L, Li J, Lawton-Rauh A, Tian D. (2011) Unusual signatures of highly adaptable R-loci in closely-related Arabidopsis species. Gene 482:24–33
    Wang J, Tan SJ, Zhang L, Li P, Tian D. (2011) Co-Variation Among Major Classes of LRR-Encoding Genes in Two Pairs of Plant Species. J Mol Evol 72:498–509
    Wu Y, Yuan HZ, Tan SJ, Chen JQ, Tian D, Yang HW (2011) Increased complexity of gene structure and base composition in vertebrates. Journal of Genetics and Genomics 38: 297-305
    Zhang X, Wang L, Yuan Y, Tian D, Yang S. (2011) Rapid copy number expansion and recent recruitment of domains in S-receptor kinase-like genes contribute to the origin of self-incompatibility. FEBS J 278: 4323-4337
    Zhang X, Feng Y, Chen H, Tian D, Yang S, Chen J-Q (2011) Relative evolutionary rates of NBS-encoding genes revealed by soybean segmental duplication. Mol Genet Genomics 285: 79-90
    Yang H, Zhong Y, Peng C, Chen JQ, Tian D. (2010) Important role of indels in somatic mutations of human cancer genes. BMC Med Genet 11:128
    Yue J-X, Li J, Wang D, Araki H, Tian D, Yang S (2010) Genome-wide investigation reveals high evolutionary rates in annual plants. BMC Plant Biol 10: 242
    Li J, Ding J, Zhang W, Zhang Y, Tang P, Chen JQ, Tian D, Yang S. (2010) Unique pattern of number evolution in gramineous NBS-LRR genes. Mol Genet Genomics 283:427–438
    Chen Q, Han Z, Jiang H, Tian D, Yang S. (2010) Strong positive selection drives rapid diversification of R-genes in Arabidopsis relatives. J Mol Evol 70: 137-148
    Tang P, Zhang Y, Sun X, Tian D, Yang S, Ding J. (2010) Disease resistance signature of the leucine-rich repeat receptor-like kinase genes in four plant species. Plant Sci 179: 399-406
    Zhang Y, Wang J, Zhang X, Chen JQ, Tian D, Yang S. (2009) Genetic signature of rice domestication shown by a variety of genes. J Mol Evol 68:393-402
    Zhu L, Zhang Y, Zhang W, Yang S, Chen JQ, Tian D. (2009) Patterns of exon-intron architecture variation of genes in eukaryotic genomes. BMC Genomics 10:47
    Yang H, Wu Y, Feng J, Yang S, Tian D (2009) Evolutionary pattern of protein architecture in mammal and fruit fly genomes. Genomics 93:90-97
    Yang S, Gu T, Pan C, Feng Z, Ding J, Hang Y, Chen JQ, Tian D (2008) Genetic variation of NBS-LRR class resistance genes in rice lines. Theor Appl Genet 116:165-177
    Zhang W, Sun X, Yuan H, Araki H, Wang J, Tian D (2008) The pattern of insertion/deletion polymorphism in Arabidopsis thaliana. Mol Genet Genomics 280:351-361
    Yang S, Zhang X, Yue JX, Tian D, Chen JQ. (2008) Recent duplication dominates the expansion of the NBS-encoding genes in two woody species Mol Genet Genomics 280: 187-198
    Du J, Gu T, Tian H, Araki H, Yang YH, Tian D (2008) Grouped nucleotide polymorphism: A major contributor to genetic variation in Arabidopsis. Gene 426:1-6
    Ding J, Zhang W, Jing Z, Chen JQ, Tian D (2007) Unique pattern of R-gene variation within populations in Arabidopsis. Mol Genet Genomics 277:619-629
    Yang S, Jiang K, Araki H, Ding J, Yang Y, Tian D (2007) A molecular isolation mechanism associated with high intra-specific diversity in rice. Gene 394:87-95
    Ding J., Cheng H., Jin Q., Araki H., Yang Y, Tian D (2007) Contrasting patterns of evolution between allelic groups at a single locus in Arabidopsis. Genetica 29:235-242
    Ding J, Araki H, Wang Q, Zhang P, Chen JQ, Tian D (2007) Highly asymmetric rice genomes. BMC Genomics 8:154
    Jiang H, Wang C, Ping L, Tian D, Yang S. (2007) Pattern of LRR nucleotide variation in plant resistance genes. Plant Science 173:253-261
    Yang S, Feng Z, Zhang X, Jiang K, Jin X, Hang Y, Chen JQ, Tian D (2006) Genome-wide investigation on the genetic variations of rice disease resistance genes. Plant Mol Biol 62:181-193
    Zhou T, Wang Y, Chen JQ, Araki H, Jing Z, Jiang K, Shen J, Tian D (2004). Genome-wide identification of NBS genes in rice reveals significant expansion of divergent non-TIR NBS Genes. Mol Genet Genomics 271:402-415
    Mauricio R, Stahl E, Korves T, Tian D, Kreitman M & Bergelson J (2003) Natural selection for polymorphism in the disease resistance gene RPS2 of Arabidopsis. Genetics 163(2):735-746
    Tian D, Niu C & Rose R. (2002) DNA transfer by highly asymmetric somatic hybridisation in Medicago truncatula x Medicago rugosa and Medicago truncatula x Medicago scutellata. Theo Appl Genet 104:9-16
    Tian D, & Rose R (1999) Plant regeneration of asymmetric somatic hybrids between annual Medicago truncatula and Medicago scutellata. Plant Cell Report 18:989-996
    Tian D (1994) 杂交水稻制种高产栽培技术. 四川科技出版社
    Tian D (1991) 水稻异交栽培学. 四川科技出版社
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